-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_16422848-16587705

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for snap_scaffold_3-snap.3172-T1
Valid prediction for GlimmerHMM_glimmerT_8042-T1
Valid prediction for GlimmerHMM_glimmerT_8038-T1
Valid prediction for snap_scaffold_3-snap.3167-T1
Valid prediction for HiQ_model.g5295.t1
Valid prediction for GlimmerHMM_glimmerT_8026-T1
Valid prediction for snap_scaffold_3-snap.3184-T1
Valid prediction for snap_scaffold_3-snap.3159-T1
Valid prediction for snap_scaffold_3-snap.3151-T1
Valid prediction for snap_scaffold_3-snap.3154-T1
Valid prediction for Augustus_model.g5301.t1
Valid prediction for GlimmerHMM_glimmerT_8035-T1
Valid prediction for snap_scaffold_3-snap.3171-T1
Valid prediction for snap_scaffold_3-snap.3177-T1
Valid prediction for CodingQuarry_transcript_46419-T1
Valid prediction for pasa_asmbl_40628.p2
Valid prediction for snap_scaffold_3-snap.3187-T1
Valid prediction for CodingQuarry_transcript_46416-T1
Valid prediction for snap_scaffold_3-snap.3182-T1
Valid prediction for CodingQuarry_transcript_46420-T1
Valid prediction for HiQ_model.g5311.t1
Valid prediction for snap_scaffold_3-snap.3180-T1
Valid prediction for Augustus_model.g5300.t1
Valid prediction for snap_scaffold_3-snap.3178-T1
Valid prediction for GlimmerHMM_glimmerT_8039-T1
Valid prediction for Augustus_model.g5316.t1
Valid prediction for GlimmerHMM_glimmerT_8031-T1
Valid prediction for snap_scaffold_3-snap.3164-T1
Valid prediction for Augustus_model.g5310.t1
Valid prediction for GlimmerHMM_glimmerT_8033-T1
Valid prediction for CodingQuarry_transcript_46418-T1
Valid prediction for snap_scaffold_3-snap.3190-T1
Valid prediction for HiQ_model.g5297.t1
Valid prediction for GlimmerHMM_glimmerT_8017-T1
Valid prediction for snap_scaffold_3-snap.3152-T1
Valid prediction for snap_scaffold_3-snap.3157-T1
Valid prediction for Augustus_model.g5298.t1
Valid prediction for GlimmerHMM_glimmerT_8020-T1
Valid prediction for GlimmerHMM_glimmerT_8037-T1
Valid prediction for GlimmerHMM_glimmerT_8043-T1
Valid prediction for Augustus_model.g5315.t1
Valid prediction for snap_scaffold_3-snap.3181-T1
Valid prediction for snap_scaffold_3-snap.3179-T1
Valid prediction for snap_scaffold_3-snap.3176-T1
Valid prediction for GlimmerHMM_glimmerT_8030-T1
Valid prediction for Augustus_model.g5299.t1
Valid prediction for snap_scaffold_3-snap.3153-T1
Valid prediction for GlimmerHMM_glimmerT_8036-T1
Valid prediction for pasa_asmbl_40630.p1
Valid prediction for CodingQuarry_transcript_46421-T1
Valid prediction for snap_scaffold_3-snap.3148-T1
Valid prediction for CodingQuarry_transcript_46417-T1
Valid prediction for snap_scaffold_3-snap.3173-T1
Valid prediction for pasa_asmbl_40622.p1
Valid prediction for GlimmerHMM_glimmerT_8021-T1
Valid prediction for Augustus_model.g5308.t1
Valid prediction for GlimmerHMM_glimmerT_8027-T1
Valid prediction for snap_scaffold_3-snap.3186-T1
Valid prediction for pasa_asmbl_40620.p1
Valid prediction for Augustus_model.g5303.t1
Valid prediction for CodingQuarry_transcript_46414-T1

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for snap_scaffold_3-snap.3162-T1
Valid prediction for Augustus_model.g5296.t1
Valid prediction for Augustus_model.g5312.t1
Valid prediction for snap_scaffold_3-snap.3160-T1
Valid prediction for GlimmerHMM_glimmerT_8044-T1
Valid prediction for GlimmerHMM_glimmerT_8024-T1
Valid prediction for snap_scaffold_3-snap.3175-T1
Valid prediction for snap_scaffold_3-snap.3169-T1
Valid prediction for snap_scaffold_3-snap.3150-T1
Couldn't classify 148706, 149152
Sorry, prediction pasa_asmbl_39509.p1 fails validation.
(AGA)	 GC	148706-149152	CC	GCC
Valid prediction for snap_scaffold_3-snap.3166-T1
Valid prediction for pasa_asmbl_39513.p2
Valid prediction for snap_scaffold_3-snap.3158-T1
Valid prediction for Augustus_model.g5304.t1
Valid prediction for snap_scaffold_3-snap.3170-T1
Valid prediction for snap_scaffold_3-snap.3161-T1
Valid prediction for snap_scaffold_3-snap.3185-T1
Valid prediction for snap_scaffold_3-snap.3188-T1
Valid prediction for Augustus_model.g5305.t1
Couldn't classify 67109, 67222
Sorry, prediction pasa_asmbl_39511.p1 fails validation.
(GCA)	 CG	67109-67222	GT	AGG
(TGG)	 AG	67908-68033	GT	AGG
(GGC)	 AG	68226-68474	TT	GAT
-recovered pasa_asmbl_39511.p1, terminal, 68226, 68474
-recovered pasa_asmbl_39511.p1, internal, 67908, 68033
Valid prediction for CodingQuarry_transcript_46422-T1
Valid prediction for GlimmerHMM_glimmerT_8025-T1
Valid prediction for HiQ_model.g5314.t1
Valid prediction for snap_scaffold_3-snap.3156-T1
Valid prediction for Augustus_model.g5313.t1
Valid prediction for GlimmerHMM_glimmerT_8029-T1
Valid prediction for snap_scaffold_3-snap.3189-T1
Valid prediction for GlimmerHMM_glimmerT_8034-T1
Valid prediction for snap_scaffold_3-snap.3149-T1
Valid prediction for snap_scaffold_3-snap.3168-T1
Valid prediction for snap_scaffold_3-snap.3163-T1
Valid prediction for GlimmerHMM_glimmerT_8022-T1
Valid prediction for GlimmerHMM_glimmerT_8023-T1
Valid prediction for GlimmerHMM_glimmerT_8041-T1
Valid prediction for CodingQuarry_transcript_46415-T1
Valid prediction for GlimmerHMM_glimmerT_8028-T1
Valid prediction for GlimmerHMM_glimmerT_8018-T1
Valid prediction for Augustus_model.g5306.t1
Valid prediction for Augustus_model.g5307.t1
Valid prediction for snap_scaffold_3-snap.3155-T1
Couldn't classify 146509, 146538
Couldn't classify 147952, 148154
Sorry, prediction pasa_asmbl_39510.p1 fails validation.
(GGA)	 TA	146509-146538	GT	AGG
(GTT)	 AG	146835-146865	GT	AGG
(ATA)	 AG	146987-147157	GT	AGG
(ACA)	 AG	147599-147838	GT	CGG
(ATG)	 AG	147952-148154	AG	AGA
-recovered pasa_asmbl_39510.p1, internal, 146835, 146865
-recovered pasa_asmbl_39510.p1, internal, 146987, 147157
-recovered pasa_asmbl_39510.p1, internal, 147599, 147838
Valid prediction for GlimmerHMM_glimmerT_8019-T1
Valid prediction for pasa_asmbl_39507.p1
Valid prediction for GlimmerHMM_glimmerT_8032-T1
Valid prediction for GlimmerHMM_glimmerT_8040-T1
Valid prediction for snap_scaffold_3-snap.3183-T1
Valid prediction for snap_scaffold_3-snap.3165-T1
Couldn't classify 149309, 149956
Sorry, prediction pasa_asmbl_39508.p1 fails validation.
(AAA)	 AC	149309-149956	TT	CTT
Valid prediction for Augustus_model.g5309.t1
Valid prediction for Augustus_model.g5302.t1
Valid prediction for snap_scaffold_3-snap.3174-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8529, rend_intergenic: 2941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65028, rend_intergenic: 64245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83679, rend_intergenic: 80983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112794, rend_intergenic: 110892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131722, rend_intergenic: 129565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159629, rend_intergenic: 155173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 164858
-exon list size: 329


building trellis

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3.9    
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6.0    
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6.9    
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8.8    
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10.9    
11.2    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
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13.6    
13.9    
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18.4    
18.7    
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23.6    
23.9    
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25.7    
26.0    
26.3    
26.6    
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27.8    
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29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
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31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.8    
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34.4    
34.7    
35.0    
35.3    
35.6    
36.0    
36.3    
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38.4    
38.7    
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39.9    
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42.0    
42.3    
42.6    
42.9    
43.2    
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44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
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54.1    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.5    
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58.0    
58.3    
58.6    
58.9    
59.2    
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60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
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62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
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67.1    
67.4    
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68.0    
68.3    
68.6    
68.9    
69.2    
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70.4    
70.7    
71.0    
71.3    
71.6    
71.9    
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73.1    
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74.0    
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74.6    
74.9    
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80.4    
80.7    
81.0    
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81.6    
81.9    
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83.1    
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84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.1    
93.4    
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94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
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96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 8529, rend_intergenic: 2941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65028, rend_intergenic: 64245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83679, rend_intergenic: 80983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112794, rend_intergenic: 110892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131722, rend_intergenic: 129565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159629, rend_intergenic: 155173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support